Sequence
atgc intronic sequence ATGC exonic sequencegtacggatagttttgttcattcagtaattatgtgtctaaactagtaaatgcacagcggttataatgttttaccctatttaaattttatgcatgtttgggtttccgaaggtgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG
Basic information
species | Physcomitrella patens |
transcript | PP1S34_305V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S34_305V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
gtacggatagttttgttcattcagtaattatgtgtctaaactagtaaatgcacagcggttataatgttt-taccctatttaaattttatgcatgtttgggtttccgaaggtgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG----------------------------------------------
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------------------------------------------------------------gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgtt-ttgttttgtaacttacaaatgtcttggttttcctcttatca-----gGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
upper sequence: PP1S34_305V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07730 (Selaginella moellendorffii), 3'ss of exon 3
gtacggatagttttgttcattcagtaattatgtgtctaaactagtaaatgcacagcggttataatgttttaccctatttaaattttatgcatgtttgggtttccgaaggtgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG
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--------------------------------------------------------------------------------------------gtatgaattt--gggggttttcct-ctggtctctgggctgaaattaggtt-ttttggct--tgaaac---agGAGGAAGCGAAAGAAGAGAGCGACGATGACATGGGCTTTAGCTTGTTCGATTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG
atttgttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggatagttttgttcattcagtaattatgtgtctaaactagtaaatgcacagcggttataatgttttaccctatttaaattttatgcatgtttgggtttccgaaggtgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA